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Selecting Reads for Haplotype Assembly

Sarah O. Fischer, View ORCID ProfileTobias Marschall
doi: https://doi.org/10.1101/046771
Sarah O. Fischer
1Center for Bioinformatics, Saarland University, Saarbrücken, Germany
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Tobias Marschall
1Center for Bioinformatics, Saarland University, Saarbrücken, Germany
2Max Planck Institute for Informatics, Saarbrücken, Germany
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Abstract

Haplotype assembly or read-based phasing is the problem of reconstructing both haplotypes of a diploid genome from next-generation sequencing data. This problem is formalized as the Minimum Error Correction (MEC) problem and can be solved using algorithms such as WhatsHap. The runtime of WhatsHap is exponential in the maximum coverage, which is hence controlled in a pre-processing step that selects reads to be used for phasing. Here, we report on a heuristic algorithm designed to choose beneficial reads for phasing, in particular to increase the connectivity of the phased blocks and the number of correctly phased variants compared to the random selection previously employed in by WhatsHap. The algorithm we describe has been integrated into the WhatsHap software, which is available under MIT licence from https://bitbucket.org/whatshap/whatshap.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted April 06, 2016.
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Selecting Reads for Haplotype Assembly
Sarah O. Fischer, Tobias Marschall
bioRxiv 046771; doi: https://doi.org/10.1101/046771
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Selecting Reads for Haplotype Assembly
Sarah O. Fischer, Tobias Marschall
bioRxiv 046771; doi: https://doi.org/10.1101/046771

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